Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma

Abstract

ABSTRACT. Melanoma is a malignant tumor and one of the most frequent metastatic cancers. This study was conducted to identify differential expression genes (DEGs) and single nucleotide variations (SNVs) in metastatic melanoma. We analyzed microarray data of GSE23056 downloaded from the Gene Expression Omnibus, including two normal samples (skinN1 and skinN2) and 2 metastatic melanoma samples (skinT and lymphT). We not only compared DEGs in metastatic melanoma samples with normal samples (lymphT_skinN and skinT_ skinN), but also compared DEGs between two metastatic melanoma types (lymphT_skinT). SNVs were identified by using BurrowsWheeler Aligner and Cufflinks in metastatic melanoma samples using RNA-seq. Sequence Alignment/Map tools and the ANNOVAR software were used to analyze and annotate SNVs. We identified 18 significantly common DEGs in lymphT_skinN and skinT_skinN and one common gene, YBX1, in lymphT_skinN, skinT_skinN, and lymphT_skinT. We identified 49,534, 48,118, 63,812, and 33,096 SNVs in skinN1, skinN2, 8154skinT, and lymphT, respectively. Twenty-nine SNVs were located in exonic regions of two DEGs, HLA-B and TSPAN10. SNVs that exist only in tumors were located in MARVELD1, SLC16A3, and VAV3. The DEGs screened in our study are potential biomarkers for metastatic melanoma therapy.

Transcriptome Analysis of Canine Cutaneous Melanoma and Melanocytoma Reveals a Modulation of Genes Regulating Extracellular Matrix Metabolism and Cell Cycle

“…Our results also suggest the activation of newly detected genes involved in the ECM-cell interaction pathway that have not yet identified in human melanoma expression studies. The RNA-seq approach has been uncommonly used to study human melanoma cell lines 18, 21, 39 and only single studies have examined human primary and metastatic melanoma tumor samples 23 . Numerous authors have demonstrated a reciprocal effect of host-tumor interactions on neoplastic and stromal cells and a synergistic effect of co-cultivation of human melanoma and stromal fibroblasts in invasive and metastatic abilities 11, 16, 40–42 .…”

“…Therefore a bidirectional interdependency seems to be fundamental in promoting tumor invasiveness and aggressiveness 16 and a multidirectional approach is essential when new anti-cancer strategies are planned and developed. The use of RNA sequencing (RNA-seq) technology has expanded the diagnostic, prognostic and therapeutic opportunities in cancer research, allowing the recognition of gene fusions and differential expression of disease-associated transcripts 17, 18 . In the melanoma field, many studies have focused on RNA-seq of melanocytes 19 and melanoma cell lines 20–22 and only very recently few of them on whole tumor samples or single malignant, immune, stromal and endothelial cells 18, 23–26 .…”

“…The use of RNA sequencing (RNA-seq) technology has expanded the diagnostic, prognostic and therapeutic opportunities in cancer research, allowing the recognition of gene fusions and differential expression of disease-associated transcripts 17, 18 . In the melanoma field, many studies have focused on RNA-seq of melanocytes 19 and melanoma cell lines 20–22 and only very recently few of them on whole tumor samples or single malignant, immune, stromal and endothelial cells 18, 23–26 . In veterinary medicine, this technique has been used in recent years to study degenerative diseases and stress-related conditions and only rarely has it applied to tumor analysis in canine head and neck carcinoma, mammary carcinoma and lymphoma 27–30 .…”

Molecular genetic response of Xiphophorus maculatus–X. couchianus interspecies hybrid skin to UVB exposure

“…These genes showed a pattern of up-regulation due to hybridization and also further up-regulation effected by UVB exposure. Among these 18 genes, 4 genes are related to melanin synthesis ( mitfa , tyr , tyrp1a , dct ), 3 genes are related to melanosome transport ( rab27 , rab38a , pmela ), 4 genes are related to pigmentation ( slc2a11b , slc24a5 , oca2, pax3b ), and 4 genes are melanoma/melanocyte marker ( tspan10 , slc45a2 , ptn , 2,8-sialyltranferase ) (Kobayashi et al, 1994; Kuroda et al, 2005; Kang et al, 2007; Zhang et al, 2013; Haltaufderhyde and Oancea 2014; Kimura et al, 2014; Liu et al, 2014; Morice-Picard et al, 2014; Choi et al, 2015; Eaton et al, 2015; Lindsay et al, 2015). The remaining two genes ( CA10 and kirrel3l ) are not well studied and their functions poorly charactrized.…”

Research Techniques Made Simple: Methodology and Clinical Applications of RNA Sequencing

“…RNA-seq has been instrumental in defining mutations and biomarkers associated with cutaneous malignancies. Liu et al (2014) performed RNA-seq analysis of cell lines derived from nonmetastatic and metastatic human melanoma tumors to define differentially expressed genes and single nucleotide variations that represent potential biomarkers for metastatic melanoma. RNA-seq was used to identify missense mutations in the spliceosome gene SF3B1 and characterize resultant RNA-splicing defects that contribute to development of uveal melanoma (Alsafadi et al, 2016;DeBoever et al, 2015).…”